Mercurial > repos > mvdbeek > bam_readtagger
comparison bam_readtagger.xml @ 0:a38447a59412 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
author | mvdbeek |
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date | Fri, 17 Feb 2017 10:54:47 -0500 |
parents | |
children | f69131f584e8 |
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1 <tool id="bam_readtagger" name="Tag alignment files" version="0.1.8"> | |
2 <description>from multiple bam files</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="0.1.8">readtagger</requirement> | |
8 </requirements> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 readtagger -t '$tag_file' -a | |
11 #for $element in $alignment_series | |
12 '$element.annotate_with':$element.r_tag:$element.m_tag | |
13 #end for | |
14 $allow_dovetailing | |
15 $keep_suboptimal | |
16 $discarded | |
17 $verified | |
18 -o '$tagged_file' | |
19 ]]></command> | |
20 <inputs> | |
21 <param name="tag_file" argument="--tag_file" type="data" format="bam"/> | |
22 <repeat name="alignment_series" title="Alignments"> | |
23 <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/> | |
24 <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> | |
25 <expand macro="tag_options"/> | |
26 </param> | |
27 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B"> | |
28 <expand macro="tag_options"/> | |
29 </param> | |
30 </repeat> | |
31 <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/> | |
32 <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/> | |
33 <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/> | |
34 <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/> | |
35 </inputs> | |
36 <outputs> | |
37 <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/> | |
38 <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string"> | |
39 <filter>verified is True</filter> | |
40 </data> | |
41 <data name="discarded_file" format="bam" from_work_dir="discarded.bam" label="Discarded reads/tags $on_string"> | |
42 <filter>verified is True</filter> | |
43 </data> | |
44 </outputs> | |
45 <tests> | |
46 <test> <!-- test that a single read originating from a pasteurianus is properly annotated in a dm6 alignment (should end in verified bam file) --> | |
47 <param name="tag_file" value="dm6.bam" ftype="bam"/> | |
48 <repeat name="alignment_series"> | |
49 <param name="annotate_with" value="pasteurianus.bam" ftype="bam"/> | |
50 <param name="r_tag" value="A"/> | |
51 <param name="m_tag" value="B"/> | |
52 </repeat> | |
53 <param name="discarded" value="True"/> | |
54 <param name="verified" value="True"/> | |
55 <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/> | |
56 <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/> | |
57 <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/> | |
58 </test> | |
59 <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) --> | |
60 <param name="tag_file" value="pasteurianus.bam" ftype="bam"/> | |
61 <repeat name="alignment_series"> | |
62 <param name="annotate_with" value="dm6.bam" ftype="bam"/> | |
63 <param name="r_tag" value="A"/> | |
64 <param name="m_tag" value="B"/> | |
65 </repeat> | |
66 <param name="discarded" value="True"/> | |
67 <param name="verified" value="True"/> | |
68 <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" /> | |
69 <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/> | |
70 <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/> | |
71 </test> | |
72 </tests> | |
73 <help><![CDATA[ | |
74 usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o | |
75 OUTPUT_FILE | |
76 | |
77 Tag reads in an alignment file based on other alignment files | |
78 | |
79 optional arguments: | |
80 -h, --help show this help message and exit | |
81 -t TAG_FILE, --tag_file TAG_FILE | |
82 Tag reads in this file. (default: None) | |
83 -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...] | |
84 Tag reads in readfile if reads are aligned in these | |
85 files.Append `:A:B` to tag first letter of tag | |
86 describing read as A, and first letter of tag | |
87 describing the mate as B (default: None) | |
88 -o OUTPUT_FILE, --output_file OUTPUT_FILE | |
89 Write bam file to this path (default: None) | |
90 | |
91 ]]></help> | |
92 </tool> |